Unfortunately, since KOMA-Script is a rather complex collection of classes and packages, problems can arise when combining third-party packages with KOMA-Script. For many of these problems solutions exist in KOMA-Script. With the package scrhack
even an extra KOMA-Script package exists to solve such problems with some packages. In case of compatibility issues between a third party package and the KOMA-Script classes, the ideal solution would of course always be to ask the author of the third party package to support the KOMA-Script classes as well as the standard classes.
Since the LaTeX kernel is developed very intensively since some years, there is also a certain risk of incompatibilities with each update of the LaTeX kernel. These are usually fixed by near-time updates of KOMA-Script classes themselves. It is recommended to check the issue tracker in case of corresponding problems to see if the problem is already known or even closed, and otherwise report a bug yourself.
Some compatibility issues are documented in more detail below:
Wiki (English): HowTo
Wiki (English): HowTo_MigrateFromStandardClass
Wiki (English): HowTo_ModernCValternatives